Multi-omics analysis on the effect of weaning on larval rearing in Chinese longsnout catfish

Chinese longsnout catfish ( Leiocassis longirostris ), endemic to the Yangtze River in China, faces germplasm depletion due to poor larval survival and growth during seedling cultivation, exacerbated by limited understanding of weaning at the molecular level. Here, the results of growth performance and digestive enzyme activity showed that live prey, such as Limnodilus spp. and Artemia nauplii was the most suitable food for first feeding. Notably, larvae fed Limnodilus spp. for more than five days could undergo sex reversal, opening up scientific avenues for the cultivation of YY supermale and all-male progeny production. For weaning, a combined feeding of live prey and microbound diet for five days was found to be more conducive. RNA-seq analysis of gastrointestinal tract (GIT) during weaning (pre-weaning, mid-weaning and post-weaning) identified 3728 differentially expressed genes enriched in protein digestion and absorption, cholesterol metabolism, starch and sucrose metabolism, and NF-kappa B signaling pathways. Furthermore, the expression patterns of appetite-regulating genes varied during weaning, with the appetite-suppressing gene cck prominently expressed during the mid-weaning and appetite-stimulating genes npy and agrp significantly upregulated during the post-weaning. 16S rRNA sequencing revealed the establishment of a stable core microbial community in the GIT during weaning, with increasing richness and diversity as the weaning progressed, dominated by Proteobacteria, Bacteroidota, and Firmicutes. In conclusion, this study contributed to improving early survival and growth performance of L. longirostris and provided valuable insights into the effects of weaning on body metabolism and intestinal microbial community in farmed carnivorous fish. • Analyzed four first feeding diets and determined optimal co-feeding duration during weaning in Leiocassis longirostris . • Survival and growth of larvae were influenced by type of first feeding and its co-feeding duration. • Sex reversal occurred in larvae fed Limnodilus spp. for over 5 days. • Weaning can cause changes in gastrointestinal tract metabolism and microbial communities in L. longirostris .